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- PDB-8ezh: A tethered niacin-derived pincer complex with a nickel-carbon bon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ezh | |||||||||
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Title | A tethered niacin-derived pincer complex with a nickel-carbon bond in lactate racemase R98A/R100A variant modeled with sulfite-NPN adduct | |||||||||
![]() | Lactate racemase | |||||||||
![]() | ISOMERASE / Catalytic activity / isomerase activity / racemase and epimerase activity racemase acting on hydroxy acids and derivatives / metal ion binding | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gatreddi, S. / Hausinger, R.P. / Hu, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Irreversible inactivation of lactate racemase by sodium borohydride reveals reactivity of the nickel-pincer nucleotide cofactor. Authors: Gatreddi, S. / Sui, D. / Hausinger, R.P. / Hu, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.2 KB | Display | ![]() |
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PDB format | ![]() | 75 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ezfSC ![]() 8eziC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules B
#1: Protein | Mass: 47153.289 Da / Num. of mol.: 1 / Mutation: R98A, R100A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: larA, lp_0104 / Production host: ![]() |
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-Non-polymers , 7 types, 223 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/ENJ.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ENJ.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ENJ / ( | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-NI / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.72 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Sodium HEPES/MOPS (pH 7.5), 60 mM Magnesium chloride hexahydrate, 60 mM Calcium chloride dihydrate, 27% Ethylene glycol and 14% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→37.79 Å / Num. obs: 29029 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.74 / Rpim(I) all: 0.24 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 9.1 % / Rmerge(I) obs: 4.7 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2074 / Rpim(I) all: 1.62 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8EZF Resolution: 1.99→37.79 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→37.79 Å
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Refine LS restraints |
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LS refinement shell |
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